8U7B
Crystal structure of Apo form of Short Prokaryotic Argonaute TIR-APAZ (SPARTA) heterodimer
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293.15 | 0.1 M sodium acetate, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.61 | 73.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 197.181 | α = 90 |
b = 197.181 | β = 90 |
c = 183.407 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2022-07-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.979338 | NSLS-II | 17-ID-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 2.66 | 170.76 | 96.2 | 0.148 | 0.042 | 0.999 | 13.7 | 13.3 | 40914 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.66 | 2.99 | 1.767 | 0.554 | 0.572 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.66 | 49.71 | 1.35 | 40895 | 2070 | 67.56 | 0.1823 | 0.1793 | 0.2387 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.947 |
f_angle_d | 0.608 |
f_chiral_restr | 0.044 |
f_plane_restr | 0.004 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7365 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |